☰ Navigation Tabs
Structure of human ceramide synthase 6 (CerS6) bound to C16:0 (nanobody Nb02)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QZ6
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.3667 f_angle_d 0.6304 f_chiral_restr 0.0382 f_plane_restr 0.0092 f_bond_d 0.0023
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 153485 Reported Resolution (Å) 3.02 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (8QZ6) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 56.36
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.1 CTF CORRECTION RELION 3.1.3 MODEL FITTING UCSF ChimeraX 1.4 MODEL FITTING Coot 0.9.8 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION RELION 3.1.3 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4497470